[tdwg-content] [tdwg-tag] canonicalScientificName

Sat Mar 17 10:23:33 CET 2012

Dear All,
just a little side note: as a user of names - mostly animal (insect) but
sometimes plant and fungi names - I am happiest when I can see the verbatim
original name in the record, including the source from where it was taken
(e.g., collection label) and the identifier. This gives me the best basis
for a correct name interpretation.
An additional canonical, - i.e. a standard name may be helpful, - but only
if it comes with a reference and with annotations how that interpretation
was done (automated, manually, by an expert, etc.).
In my own database (mainly on ground beetles) I am using a field for
'verbatimOriginalName', another field for my interpreted 'standard' name
based on my own current checklist (which is regularly updated), and a third
field "nameGUID". For me, a nameGUID is a stable readable unique name
string with the Code-compliant "anchor name" (the binomen that denotes the
name-bearing type) always included. With a few additional symbols, I can
annotate replacement names, subsequent combinations, homonyms (incl.
cross-rank & cross-domain homonyms), etc. that can cause confusion in a
database (Just think of a mixture of species names, where the genus are
homonyms, e.g. in the case of genus Notiophilus. You can study plenty of
such unresolved mixtures in GBIFs or EOL...)

Best wishes,
Wolfgang
------------------------------------

Wolfgang Lorenz, Tutzing, Germany

Am 17. März 2012 02:25 schrieb Peter Desmet <peter.desmet at umontreal.ca>:

> Hi Chuck and others,
>
> I submitted a formal request [1] to add the term canonicalScientificName
> to hopefully reach a consensus from the TDWG community: either we add it or
> we don't. This term keeps popping up and I think it would be good if we
> reached a formal decision [2]. So I'm all for keeping the discussion open
> and involving more actual users. Given the reactions (pro and con) it
> wouldn't help much if I retract my request now I think.
>
> Me personally am very happy with the response I got so far. I now think
> that the need for the term (with the definition I proposed) is no longer
> justified, on the condition that we refine the definition for genus, which
> I also formally requested [3]. Darwin Core is a community standard and I
> just want to improve it where I can: Is there a way to share canonical
> names? Is it even necessary? The eventual solution (don't do anything, add
> canonicalScientificName as is or altered, or change the definition for
> genus) is a community decision.
>
> Cheers,
>
> Peter
>
>
> [1] http://code.google.com/p/darwincore/issues/detail?id=150
> [2] http://rs.tdwg.org/dwc/terms/history/decisions/index.htm
> [3] http://code.google.com/p/darwincore/issues/detail?id=151
>
> On Fri, Mar 16, 2012 at 18:18, Chuck Miller <Chuck.Miller at mobot.org>wrote:
>
>> Peter,****
>>
>> Are you now withdrawing your formal request to add the term
>> canonicalScientificName to DwC?  I had forwarded your request to John
>> Wieczorek to notify him of the initiation of the change process on Google
>> Code.****
>>
>> ** **
>>
>> Frankly, I was hoping for a broader comment period involving more of the
>> actual “users” that have been mentioned in the various threads,
>> particularly more of the plant name users, to put some more balance into
>> the discussion.  Then, let the process go through to an up or down decision
>> on the request based on that (hopefully) broader discussion.  Discounting
>> hybrid names as “an edge case” seemed a bit edgy and worthy of some more
>> reaction from actual users/consumers of plant name data before being taken
>> as consensus.****
>>
>> ** **
>>
>> But, are you withdrawing the request?  ****
>>
>> ** **
>>
>> Thanks,****
>>
>> Chuck****
>>
>> ** **
>>
>> *From:* tdwg-tag-bounces at lists.tdwg.org [mailto:
>> tdwg-tag-bounces at lists.tdwg.org] *On Behalf Of *Peter Desmet
>> *Sent:* Friday, March 16, 2012 4:52 PM
>> *To:* Tim Robertson [GBIF]
>> *Cc:* TDWG content mailing list; tdwg-tag at lists.tdwg.org
>> *Subject:* Re: [tdwg-tag] [tdwg-content] canonicalScientificName****
>>
>> ** **
>>
>> Hi all,****
>>
>> ** **
>>
>> The reason why I proposed a canonicalScientificName was to make it easier
>> for data users.****
>>
>> ** **
>>
>> As Tim Robertson points out [1], adding this term will probably make it
>> more complicated, without much benefit. Gregor Hagedorn [2] explains that
>> canonicalScientificName is not a solution for some edge cases (like
>> hybrids) and infraspecific names without a rank marker don't mean much in
>> botany. Rich Pyle [3] points out that more requests will probably be
>> proposed (canonicalScientificNameWithoutRanks,
>> canonicalScientificNameWithoutInfrageneric), demonstrated by Gregor's
>> remark [2].****
>>
>> ** **
>>
>> I now agree with all of these. The only thing I'd like to refine is the
>> definition for genus [4], for which I issued a request:
>> http://code.google.com/p/darwincore/issues/detail?id=151****
>>
>> ** **
>>
>> See my argumentation in the link above. Basically: As I explained before
>> (and Markus Döring before me), under the current definition the genus gets
>> populated with the genus name of the accepted taxon for a synonym, while
>> the specificEpithet and infraspecificEpithet are not. I think this is
>> counter intuitive and confusing. I would populate it with the "genus name
>> of the scientificName", which I think is how much people interpret it
>> anyway. Advantages:****
>>
>> ** **
>>
>> 1. Agreeing with the refined definition for genus won't affect most of
>> our applications and data (only for those who cared about putting the
>> accepted genus for synonyms).****
>>
>> 2. No new term canonicalScientificName.****
>>
>> 3. Not need to update the useful definition for scientificName (verbose
>> all the way if you can).****
>>
>> 4. Publishers and aggregators *have the option* to provide an easier to
>> use name via genus, specificEpithet and infraspecificEpithet. None of these
>> have an authorship, so creating a canonicalScientificName under the
>> proposed definition is as easy as TRIM(genus+" "+specificEpithet+"
>> "+infraspecificEpithet).****
>>
>> 5. The above statement only applies to genera, species and infraspecific
>> taxa, but this is the bulk of our data. This method cannot be applied to
>> infrageneric taxa and higher taxa, but as Rich pointed out [3], there are
>> alternative methods for this.****
>>
>> 6. Aggregators can ignore genus, specificEpithet and infraspecificEpithet
>> for heterogenous networks and use parsers to deal with scientificNames.
>> Stripping out the scientificNameAuthorship or using a simple regular
>> expression won't sometimes be enough of course, e.g. "*Calamagrostis* *
>> stricta* (Timm) Koeler subsp. *stricta* (Timm) Koeler var. *borealis*(Laestadius) Hartman" and those pesky hybrids. The good this is that once
>> they have done the work, they can actually express that data in Darwin Core
>> (see point 4).****
>>
>> 7. Timon lepidus won't complain [5]. :-)****
>>
>> ** **
>>
>> Regards,****
>>
>> ** **
>>
>> Peter****
>>
>> ** **
>>
>> [1] http://code.google.com/p/darwincore/issues/detail?id=150#c1****
>>
>> [2] http://code.google.com/p/darwincore/issues/detail?id=150#c3****
>>
>> [3] http://lists.tdwg.org/pipermail/tdwg-tag/2012-March/002487.html****
>>
>> [4] http://rs.tdwg.org/dwc/terms/index.htm#genus****
>>
>> [5] https://plus.google.com/114672072317054763788/posts/Nph2ksggNZW****
>>
>> ** **
>>
>> On Thu, Mar 15, 2012 at 17:28, Peter Desmet <peter.desmet at umontreal.ca>
>> wrote:****
>>
>> Hi all,****
>>
>> ** **
>>
>> Since most of the discussion happened on this tdwg-content and tdwg-tag
>> mailing lists already, can't we continue here? I created a link to both
>> from the issue page:
>> http://code.google.com/p/darwincore/issues/detail?id=150#c2****
>>
>> ** **
>>
>> I have been stuck in a meeting all day, while Tim Roberston wrote some
>> convincing arguments against creating a canonicalScientificName term (
>> http://code.google.com/p/darwincore/issues/detail?id=150#c1), as did
>> Rich Pyle (email March 14 17:20 GMT-10:00). I will need some time to
>> think about these. :-) I will try to write a coherent response tomorrow.*
>> ***
>>
>> ** **
>>
>> Peter****
>>
>> ** **
>>
>>  ****
>>
>> --
>> Peter Desmet
>> Biodiversity Informatics Manager
>> Canadensys - www.canadensys.net
>>
>> Université de Montréal Biodiversity Centre
>> 4101 rue Sherbrooke est
>> Montreal, QC, H1X2B2
>> Canada
>>
>> Phone: 514-343-6111 #82354
>> Fax: 514-343-2288
>> Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
>> Skype: anderhalv
>> Public profile: http://www.linkedin.com/in/peterdesmet****
>>
>> _______________________________________________
>> tdwg-tag mailing list
>> tdwg-tag at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>>
>>
>
>
> --
> Peter Desmet
> Biodiversity Informatics Manager
> Canadensys - www.canadensys.net
>
> Université de Montréal Biodiversity Centre
> 4101 rue Sherbrooke est
> Montreal, QC, H1X2B2
> Canada
>
> Phone: 514-343-6111 #82354
> Fax: 514-343-2288
> Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
> Skype: anderhalv
> Public profile: http://www.linkedin.com/in/peterdesmet
>
> _______________________________________________
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>
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